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Category Archives: Calcium Imaging
There is no recipe for discoveries
There is no recipe for discoveries, and there is no cookbook on how to publish a paper. But at least there are typical events and routes that are often encountered. Here, I’d like to share the trajectory of a study … Continue reading
Posted in Calcium Imaging, Data analysis, hippocampus, Imaging, machine learning, Microscopy, neuroscience, Review
Tagged Calcium Imaging, Data analysis, Microscopy
8 Comments
Why your two-photon images are noisier than you expect
A gallery of calcium imaging recordings of neurons and astrocytes with single noisy frames on the left and averaged beautiful noise-free images on the right side. Continue reading
Posted in Calcium Imaging, Data analysis, hippocampus, Imaging, Microscopy, Neuronal activity, neuroscience, zebrafish
Tagged Calcium Imaging, Data analysis, Microscopy, photons, Scanning, zebrafish
22 Comments
Improving the resonant scanner’s sync signal using a phase locked loop (PLL)
Calcium imaging with two-photon point scanning is the technique to chronically record from identified neurons in the living brain of animals. The central piece of two-photon point scanning microscopes is a scan engine. This can be a complex optical device … Continue reading
Posted in Calcium Imaging, Imaging, Microscopy, neuroscience
Tagged Microscopy, photons, Scanning
6 Comments
Interesting papers on behavioral timescale synaptic plasticity (experiments)
Behavioral timescale synaptic plasticity (BTSP) is a form of single-shot learning observed in hippocampal place cells in mice (Bittner et al., 2015, 2017). The idea is that post-synaptic activations (“eligibility traces”) are potentiated by a dendritic plateau potential/burst (“instructive signal”) … Continue reading
Interesting papers on online motion correction for calcium imaging
In a living animal, the brain is moving up and down in the skull. This brain motion can be due to breathing, heartbeat, tongue movements, but also due to changes of posture or running. For each brain region and posture, … Continue reading
Posted in Calcium Imaging, Data analysis, Imaging, machine learning, Microscopy, Neuronal activity, neuroscience
Tagged Calcium Imaging, Data analysis, Microscopy, photons, Scanning
4 Comments
Ambizione fellowship and an open PhD position
I’m glad to share that I am going to start my own junior research group at the University of Zurich in March 2023! As an Ambizione fellow, I will receive funding for my own salary, some equipment, consumables and a … Continue reading
Self-supervised denoising of calcium imaging data
This blog post is about algorithms based on deep networks to denoise raw calcium imaging movies. More specifically, I will write about the difficulties to interprete their outputs, and on how to address these limitations in future work. I will … Continue reading
Video introduction to CASCADE
A video with tutorial on CASCADE, a supervised method to infer spike rates from calcium imaging data. Continue reading
Simple geometrical optics to understand and design point-scanning microscopes
Custom-built microscopes have become more and more sophisticated over the last years to provide a larger FOV, better resolution through some flavor of adaptive optics or simply more neurons simultaneously. Professional optical engineers are hired to design the ideal lens … Continue reading
Public peer review files
Peer-review is probably the most obscure part of the publication of scientific results. In this blog post, I would like to make the point that the best way to learn about it – except by being directly involved – is … Continue reading
Posted in Calcium Imaging, Imaging, machine learning, Microscopy, Neuronal activity, Review
Tagged deep learning, Microscopy, neuroscience, peer review
2 Comments
A blog about neurophysiology 